Whitehall officials insisted the responsibility “for organising the landing, in the nearest safe harbour” must be “assumed by the maritime competent authorities in accordance with the wishes of the master of the ship”.
The comments come after Italy’s transport minister, Danilo Toninelli – member of populist Five Star movement – urged Mrs May to “assume responsibility” and take in all rescued migrants on board the Aquarius ship, because the boat is sailing under the British territory of Gibraltar.
The Foreign Office spokesman told Italy news agency ANSA: “We are deeply concerned for the welfare of 141 migrants who have been rescued from the Mediterranean by sailing vessel Aquarius.
“It is well-established that responsibility for arranging disembarkation, at a nearby safe port, is assumed by the relevant regional maritime rescue and co-ordination, and in accordance with the wishes of the ship’s master.
“The UK is committed to working with European partners long term to tackle the shared challenge of irregular migration.”
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Malta has now agreed to let the Aquarius rescue ship dock in one of its ports, ending the regional dispute over which country would accept the migrants.
The migrants will be distributed evenly across several EU countries – France, Germany, Luxembourg, Portugal and Spain – according to the European Commission.
Malta’s government in a statement said: “Malta will be making a concession allowing the vessel to enter its ports, despite having no legal obligation to do so.
“Malta will serve as a logistical base and all of the reportedly 141 migrants on board will be distributed amongst France, Germany, Luxembourg, Portugal and Spain.”
Previously, the European Commission said that as the flag state, the UK would be held responsible for taking in all 141 immigrants, but also said other circumstances must be considered.
There are a total of 67 unaccompanied minors on the Aquarius rescue ship and the migrants are mainly of Somali and Eritrean descent.
An SOS Méditerranée spokeswoman said: “The 141 rescued people are safe onboard the Aquarius, and the situation is calm.
“There are no medical emergencies, but there are two pregnant women and most are weak and exhausted from the arduous journey.”
Malta and Italy refused to give the Aquarius rescue ship permission to dock, leading to a European scuffle over which country would end up taking in the ship.
The Aquarius, operated under French charities Médecins Sans Frontières (MSF) and SOS Méditerranée, was refused permission to dock in Italy, after the country’s populist coalition government closed its ports to rescue ships.
In June, Italy rejected an Aquarius rescue ship holding 630 migrants, leaving them stranded at sea for one week until Spain granted them permission to dock at a port in Valencia.
This is the first time Mrs May faced backlash with an EU member state, insisting the UK accept their demand to act.
The British government chooses to resettle refugees from non-EU countries neighbouring conflict territories, and so receives fewer asylum applications than its European counterparts.
A policy paper published by the Department for Exiting the EU in 2017 pledged that Britain will continue to cooperate with the EU in resolving migration issues.